[phenixbb] ncs

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Sat Jun 27 14:46:11 PDT 2009

> > By the way, I have  excessive_distance_limit = None. If I 
> > change it to some number, how does it work? the violating residues will 
> > be  excluded or the whole molecule will?
> >   
> I'm not sure, Ralf knows this better. Ralf, could you comment on this 
> please?
> My guess, that all this parameter does is it checks the distances 
> between atoms in NCS copies and if there is a distance larger than 
> excessive_distance_limit, then phenix.refine stops and tells you this.

Yes, that's correct. The distance check is just to alert you to the
problem; it is not trying to be smart about fixing it. You have to
do it yourself with the atom selection syntax ("and", "or", "not").

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